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Zinc in PDB 3ugd: Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta

Enzymatic activity of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta

All present enzymatic activity of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta:
2.7.11.13;

Protein crystallography data

The structure of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta, PDB code: 3ugd was solved by S.Shanmugasundararaj, T.Stehle, K.W.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.96 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.946, 32.504, 49.677, 90.00, 94.21, 90.00
R / Rfree (%) 17.3 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta (pdb code 3ugd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta, PDB code: 3ugd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ugd

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Zinc binding site 1 out of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:8.6
occ:1.00
 ND1 A:HIS269 2.1 8.6 1.0
SG A:CYS272 2.3 9.1 1.0
SG A:CYS247 2.3 8.6 1.0
SG A:CYS244 2.4 8.0 1.0
CB A:CYS244 3.0 8.4 1.0
CE1 A:HIS269 3.0 8.2 1.0
CG A:HIS269 3.2 7.6 1.0
CB A:CYS247 3.3 8.6 1.0
CB A:CYS272 3.4 8.0 1.0
CB A:HIS269 3.5 7.3 1.0
N A:CYS247 3.9 8.1 1.0
N A:HIS269 4.0 7.0 1.0
CA A:CYS247 4.2 8.5 1.0
NE2 A:HIS269 4.2 8.2 1.0
CD2 A:HIS269 4.3 8.7 1.0
CA A:HIS269 4.4 7.6 1.0
CA A:CYS244 4.5 7.4 1.0
CA A:CYS272 4.7 8.5 1.0
CB A:HIS246 4.7 10.0 1.0
C A:CYS247 4.9 8.9 1.0
CD2 A:HIS246 4.9 11.2 1.0
C A:HIS246 4.9 9.1 1.0
N A:GLY248 4.9 8.0 1.0
N A:CYS272 5.0 8.9 1.0

Zinc binding site 2 out of 4 in 3ugd

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Zinc binding site 2 out of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:10.0
occ:1.00
 ND1 A:HIS231 2.1 9.6 1.0
SG A:CYS264 2.3 9.2 1.0
SG A:CYS280 2.3 11.0 1.0
SG A:CYS261 2.4 9.9 1.0
CE1 A:HIS231 2.9 10.4 1.0
CB A:CYS264 3.2 9.3 1.0
CB A:CYS261 3.2 8.8 1.0
CB A:CYS280 3.3 10.8 1.0
CG A:HIS231 3.3 9.2 1.0
N A:CYS264 3.7 10.3 1.0
CA A:HIS231 3.8 9.8 1.0
CB A:HIS231 3.8 9.2 1.0
CA A:CYS264 4.0 10.1 1.0
NE2 A:HIS231 4.1 10.8 1.0
O A:HOH25 4.1 11.5 1.0
CA A:CYS280 4.2 11.2 1.0
CD2 A:HIS231 4.3 9.8 1.0
N A:HIS231 4.6 8.9 1.0
CB A:ASP263 4.6 13.3 1.0
CA A:CYS261 4.7 8.6 1.0
N A:ARG232 4.7 11.9 1.0
C A:ASP263 4.7 11.1 1.0
C A:CYS264 4.8 9.1 1.0
C A:HIS231 4.8 10.9 1.0
CB A:MET266 4.8 8.2 1.0
N A:GLY265 4.9 7.8 1.0
C A:CYS280 5.0 10.9 1.0

Zinc binding site 3 out of 4 in 3ugd

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Zinc binding site 3 out of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:8.4
occ:1.00
 ND1 B:HIS269 2.1 8.2 1.0
SG B:CYS272 2.2 8.9 1.0
SG B:CYS247 2.3 8.0 1.0
SG B:CYS244 2.4 7.4 1.0
CB B:CYS244 3.0 8.2 1.0
CE1 B:HIS269 3.0 8.4 1.0
CG B:HIS269 3.2 7.2 1.0
CB B:CYS247 3.3 8.7 1.0
CB B:CYS272 3.3 8.3 1.0
CB B:HIS269 3.5 7.4 1.0
N B:CYS247 3.9 8.3 1.0
N B:HIS269 4.0 7.8 1.0
CA B:CYS247 4.2 8.8 1.0
NE2 B:HIS269 4.2 7.8 1.0
CD2 B:HIS269 4.3 7.8 1.0
CA B:HIS269 4.4 7.5 1.0
O B:HOH6 4.5 15.0 1.0
CA B:CYS244 4.5 8.1 1.0
CA B:CYS272 4.7 7.8 1.0
CB B:HIS246 4.8 10.5 1.0
CD2 B:HIS246 4.9 11.7 1.0
C B:CYS247 4.9 9.1 1.0
N B:CYS272 4.9 8.1 1.0
C B:HIS246 5.0 10.4 1.0
N B:GLY248 5.0 7.3 1.0

Zinc binding site 4 out of 4 in 3ugd

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Zinc binding site 4 out of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:10.0
occ:1.00
 ND1 B:HIS231 2.1 11.0 1.0
SG B:CYS264 2.3 9.7 1.0
SG B:CYS280 2.3 12.8 1.0
SG B:CYS261 2.4 9.3 1.0
CE1 B:HIS231 2.9 10.6 1.0
CB B:CYS261 3.2 9.1 1.0
CB B:CYS264 3.2 8.3 1.0
CG B:HIS231 3.3 10.4 1.0
CB B:CYS280 3.3 12.7 1.0
CA B:HIS231 3.7 11.4 1.0
CB B:HIS231 3.7 10.8 1.0
N B:CYS264 3.7 9.5 1.0
CA B:CYS264 4.1 9.2 1.0
O B:HOH8 4.1 15.5 1.0
NE2 B:HIS231 4.1 9.9 1.0
CA B:CYS280 4.2 11.8 1.0
CD2 B:HIS231 4.3 10.5 1.0
N B:HIS231 4.5 11.6 1.0
CB B:ASP263 4.6 14.2 1.0
N B:ARG232 4.6 12.8 1.0
CA B:CYS261 4.6 8.7 1.0
C B:ASP263 4.7 11.0 1.0
C B:HIS231 4.8 12.1 1.0
C B:CYS264 4.8 9.4 1.0
CB B:MET266 4.8 7.0 1.0
N B:GLY265 4.9 7.9 1.0
CA B:ASP263 5.0 12.7 1.0
C B:CYS280 5.0 11.3 1.0

Reference:

S.Shanmugasundararaj, J.Das, W.S.Sandberg, X.Zhou, D.Wang, R.O.Messing, K.S.Bruzik, T.Stehle, K.W.Miller. Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta Biophys.J. V. 103 2331 2012.
ISSN: ISSN 0006-3495
PubMed: 23283232
DOI: 10.1016/J.BPJ.2012.10.034
Page generated: Sat Oct 26 17:17:48 2024

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